Wake Up Shepard
by ManwitaPlan
Summary: My version of how ME3 should have ended.Were there really three choices? Or is that just what the Reapers wanted to see? A new take on the ending tat will take Shepard to new emotional triumphs, and heartbreaking lows. The ending I believe Mass Effect fans deserve and hopefully I'm here to deliver. Includes post choice scenes.
1. The Choice

**Hi everyone, this is an interpretation of the controversial ME3 ending I've had swimming around in my head for a while now. Hopefully it will help alleviate any of the pain you may have felt after the ending or its extended cut. Instead of just stating my Shepard's history, personality, romances and past actions here, I'm going to attempt to show all that in the story. Hopefully by the end you'll know exactly who my John Shepard really is. This first chapter is gonna be mostly a trilogy recap, hopefully giving enough information to give you guys a semi-clear picture of what's going on. All characters, and events from the games and books belong to Bioware. **

"The paths are open but you have to choose."

_But how do I choose?_

Commander John Shepard stood at the precipice of history. He was at the verge of making the most important decision in galactic history. Control, Synthesis, or Destroy, three different options. It all seemed so surreal for him. The Reapers were always the enemies, incomprehensible behemoths lurking in the dark of space, exterminating civilized life in the galaxy simply because they could. They gave no reason other than "you cannot comprehend our reasons, we are you salvation through destruction."

_Am I betraying the sacrifices of those who've died by siding with the enemy? Or am I being selfish by choosing to destroy them?_

Shepard had always been that way, thinking of others before himself. Ever since he was a child growing up on Mindoir he had always done the right thing, but now, which one is the right choice?

It was so much easier when the Reapers were just pure evil, dark Gods amusing themselves through death and destruction, but terrible revelations were made. First the Leviathans, the true masters of the galaxy, revealing the Reapers to be nothing more than former servants overthrowing their masters. Then the Catalyst showing the Reapers true colors, slaves to programming, unable to reasoned with because it is their purpose. To continue life in any way necessary, even at the expense of free will and true organic form. Yet it just didn't add up. Why was this all hidden until now. How was this information never uncovered. And where were the Leviathans during the final battle? They had given their word to assist the Galaxy, yet they never showed up. But back to the matter at hand. Shepard started slowly moving forward.

_Okay, control, synthesis, or destroy. It feels like a betrayal if I don't destroy, yet I can't doom the galaxy to the loss of it's technology, the relays, the Citadel. I, I just can't. Synthesis also just doesn't feel right either. Who am I to decide if organics should be synthesized? The beauty of organics is our imperfections, and our ability to learn and grow from them. Merging with technology would just take away from that wouldn't it? So control then. I'll force the Reapers to stop and that will be that. Okay here we go._

Shepard started moving towards the control station. As he did he noticed a faint buzzing noise in the back of his head. He stopped for a moment looking to the sides and eventually behind him, trying to figure out what was going on. As he looked round he caught glimpses of the battle outside.

That must have been the noises Shepard was hearing. It seemed that the fight was turning in favor of the Reapers. Things we're not looking good for the fragile galactic alliance he had managed to put together. He could see the Human warships side by side with Turian fighters and Asari cruisers. He smiled for a moment imaging the hell the Krogan must have been giving the reapers back down on earth. It must have been an increasingly odd sight, the Krogan fighting side by side with Asari, Turians, and the few brave STG Salarians who spited the Dalatrass and joined the fight anyway. It was an unlikely alliance to be sure, one built on the past actions of the last three years. His mind briefly drifted to all of the sacrifices that had led him to this point.

Mordin, who had given his life to atone for his guilt and cure the Genophage. To think Shepard had almost stopped him too, had pulled his gun on the good doctor, thinking that an alliance with the Salarian Union was worth condemning the Krogan race to damnation. Yet it was so much more, more than the numbers, more than these theoretical war assets. Winning the war was not worth stomping on an entire civilization. Not to him, not now, not ever. _Even if we all die here, you were right Mordin. The Krogan deserved a chance, and even if we can't stop them at least you were able to give it to them, even if briefly._

There was Thane, dying at the hands of the bastard assassin Kai Leng. His death ensuring the survival of the Salarian Councilor Valern. With Valern surviving the assassination attempt, Shepard was able to convince the other two councilors and Kaidan Alenko that he was not working with Cerberus during the Citadel coup. That is was actually Donnell Udina who had betrayed them all. At the end Thanes sacrifice was worth it, the councilors were saved, Udina met his end at barrel of Shepard's rifle. _Thank you Thane, for everything. I would have never thought that an assassin would also be someone I looked to as a role model and a friend. I'll miss the chats we used to have in the Normandy._

Then he thought of Ashley. It was still to this day the most difficult decision he had ever made. Who lives and who dies. It had to be her though. She was with the bomb. Someone needed to make sure it went off. It was their only chance to stop Saren from creating an army of mindless Krogan. _I can still hear her voice even to this day, knowing that the man she loved was leaving her to die. _He could remember every time he would talk with her next to the lockers. He could remember how they could go on for hours talking about life, love, poetry, and her sister. He remembered having to choose between Liara and Ash. He could remember it all. He remembered breaking down by himself, after she died. He remembered after sentencing the girl loved to die, the Council took away his ship and publicly humiliated him, claiming he was rash and unstable and that he would only cause greater damage. Yet he still chose to save them.

A large explosion occurred near the Crucible, jolting Shepard out of his semi day-dream. He started moving closer and closer towards the control panel. The closer and closer he got, he noticed that more and more Reapers surrounded the Crucible. The buzzing in his head steadily grew louder.

He was only about ten feet from the console. He could see his fate in front of him. He would die, but he would live. He could tell the Reapers to leave and never return. He would allow galactic life to happen as it was meant to, on its own. The buzzing continued to grow louder and louder. Shepard was having a difficult time concentrating. The Catalyst materialized next to him as he got closer to the console.

"You're making a good decision Shepard." There was something different about the way the Catalyst spoke this time. He could hear something behind his voice, something he couldn't quite place. "How do I know I'm making the right choice?" "Watch" The Catalyst waved his hand, and Shepard began to see visions. Shepard watched as the Reapers began to rebuild the Citadel, as Humanity began to build for the future, he saw the rebuilt Krogan civilization, he saw the Reapers leaving, he saw his crew mourning him, placing his nameplate on the memorial wall. Yet there was one more thing he saw. He saw the Geth, and he saw the Quarians. _Didn't the Catalyst say it wasn't possible. They could never get along. _Shepard interrupted the visions. "Wait, hold on." "What?"

"The visions showed the Geth and the Quarians together happy. Yet you said that synthetics could never work together, because it will eventually lead to death. Was the vision wrong, or are you wrong?" "We only have showed a prediction of the future, not actual events." He could hear it much more clearly this time. There was another voice behind the Catalyst, someone else was speaking. At this point the buzzing was at its loudest. "So you're lying then, you're trying to manipulate me, to agree with you." Then Shepard remembered something, something he had heard long ago, when he had first learned of the Reapers, of Indoctrination. The Reapers are believed to emit an electromagnetic wave stimulating areas of the brain and limbic system. This can result in the victim hearing whispers, seeing hallucinations, or buzzing in their head, and in extreme cases can emit a faint buzzing noise from their body.

"_Near the end, didn't James say he would hear a faint buzzing noise whenever I would walk by."_ Shepard could remember it clearly, Vega was at his usual station complaining about a buzzing noise that always seemed to pop up whenever Shepard would stop down. _"Do you even hear it Loco?" "No James I don't, maybe you're going crazy?" "Yeah that must be it Loco, that must be it." _Then Shepard took a good look at the Catalyst. It took the shape of the little biy from earth, the boy that died. The boy that Shepard had been dreaming about. No one else had seen him, and now that he thought about it, no one had paid attention to him when he got on the shuttle. _He was never there to begin with, that's why Anderson didn't see him, why those soldiers didn't see him. I've been hallucinating. _ _That's why it's always him in my dreams. The boy and the shadows._ Shepard remembered the Rachni Queen describing indoctrination with oily shadows, constantly whispering in her ears. _It all makes sense now_. Shepard looked up at the Catalyst realizing the truth. "I'm being indoctrinated." The truth hit hard, but it made sense. Shepard had been the Reapers biggest threat, it made sense to bring him onto their team. He had spent three days lying unconscious next to Object Rho, plenty of time for him to be indoctrinated. He had been on edge ever since he had destroyed the Alpha Relay.

After the Alpha Relay incident , Shepard had changed. He started drinking heavily, becoming shut in his room, rarely leaving. When Miranda had left the Normandy he became even worse, almost coming to blows with Garrus in the mess hall. He kept blaming himself, believing that he would never see her again. All those around him had believed it was due to the stress, that Shepard was finally breaking down but that wasn't it. He was being indoctrinated. All of the past events were now making sense. That's how Anderson had beaten him to the control room, that's how the Illusive Man had survived. This was all in Shepard's head.

"None of this is real, is it?" The Catalyst was stunned. "What are you talking about?" He could hear it even more now, it was a familiar voice. Whoever was truly controlling the Catalyst had spoken to Shepard before. "Stop it Shepard, you need to do this, you need to take control." "No, that's what the Illusive man wanted before he was Indoctrinated himself." Then you must synthesize." "No, that's what Saren wanted, before he became a husk." "You're being selfish Shepard, do what is necessary." _Maybe it is a coincidence. Just end it, save them all. Save Miranda. _The buzzing grew louder.

"_Shepard stop." _Shepard hesitated for a brief moment, his hands only inches away from complete control over the Reapers. _But I have to save them, I need to save everyone. "Is this really the way?" _The voice became clear; it was David Anderson, former Citadel Councilor and Mastermind of the guerilla tactics that had kept humanity alive during the struggles on Earth.

_This is the only way to stop the Reapers without damning galactic civilization. _

"_Is it? Or could it be that they are manipulating you, like they did to Saren, like they did to the Illusive Man, like the did to Amanda Kenson. Shepard the Reapers are manipulating you and you know it. Don't give up because it's become difficult, don't give up when you have come so far."_

_But it seems so easy just to control, how can we destroy all that they've built?_

"_Because they aren't who they claim, they aren't some heroic guardian angels meant to save us. They are not the former puppets of the Leviathans , who finally cut their own strings. Shepard the Leviathans don't exist."_

_But I saw them!_

"_In a vision, a vision eerily similar to what survivors describes Indoctrination to be like."_

_But they destroyed a Reaper, they promised to help us during our final attack!_

"_Yet where were they?"_

It all shattered in front of him. The Leviathans had never existed in the first place. The Reapers had been manipulating Shepard the entire time, sowing the seeds early enough to make this final indoctrination attempt seem real. Finally Shepard had his proof, enough to fight the Reapers.

"No, I don't want control, I want you dead."

"What?"

He could hear it now, the voice behind the Catalysts. The disguise had almost faded away revealing the truth. It was Harbinger, attempting to sway Shepard to his side. Shepard then turned around and started limping towards the tube containing the destroy panel. As Shepard moved towards the panel he noticed the buzzing to become quitter and quieter. The limp he was suffering from was slowly starting to fade away. He could hear more and more voices in his head, but this time they were not Reapers.

"_Wake Up Shepard, wake up."_ The more and more these voices rang out, the quieter the buzzing became until it almost completely disappeared. The Reapers that had been surrounding the station began to fade away. _"Wake up Shepard, WAKE UP!" _His limp had become a full walk, faster and faster picking up speed until he was only fifteen, maybe twenty feet away from the panel. The Catalyst materialized in front of Shepard one final time this time not even disguising his voice anymore. "Shepard you have become an annoyance. Destroy that panel and you will force our hand. We will no longer show mercy, I will hurt you. I will hurt Lawson." Shepard stared down Harbinger.

"Threating Miranda was a bad move." Shepard raised his pistol, shooting through the Catalyst, bullets piercing the tube. Shepard started slowly walking towards the panel, continually shooting, and watching as the Catalyst faded away. "_WAKE UP SHEPARD, WAKE UP!" _He continued to fire until small eruptions began inside the tube. Gradually they became larger and larger, enveloping the tube itself and eventually Shepard too. As the blinding red and white light approached him Shepard could only hear one thing.

_"Wake up Shepard, wake up." _


	2. Shepard and the Soldiers

**Hi again everyone, so hopefully with that last chapter I was able to reveal enough about my Shepard to give you all a place to jump off of. So this is going to be an Inodctrination theory story. I'm going to attempt to bring back the themes of the original Mass Effect with this "ending." Fans of Soverign may recognize a lot of the ideas he presented on Virmire are given the proper treatment. Oh and a very special character will be making an appearance. Okie everyone lets what happens once Shepard wakes up.**

"_Wake up Shepard, wake up!"_

He took a single breath, breathing in the dust and ash, and smoke in the desolated Earth's atmosphere. He was alive. Shepard opened his eyes slowly, taking in the sights around him. He was lying in a pile of dirt and stone. Remnants of the laser blast Harbinger had hit him with. It was a miracle Shepard was still alive considering that Reaper lasers can blow a hole clean through a ship. Shepard looked down at his chest, his armor cracked and bloody, yet he was still alive. He had beaten Indoctrination, he hadn't succumbed. He attempted to slowly move, using one limb at a time. First he moved his left arm, and then he moved to his right. _Okay, good, I can still move my arms. _Shepard then looked down to his legs. They were slightly covered in stone. He first attempted to slide the right leg out. Inching his leg out of the rocks, Shepard was surprised to find full movement. With one leg free he then slid the other one out, just as slowly as the first. _Okay, where am I? _Looking around all he could see was dust and smoke. His ears still ringing with sound of Harbingers laser he realized he was right near the lift into the Citadel.

As Shepard stood up his hearing started to return to him. He could hear gunfire ringing out, mixed with the shouting of man against the screeching of husks. He could hear ships flying and the sound of the Reapers lasers firing. Surveying the battlefield he concluded that Harbinger had knocked him back about 400 feet. He was flung into a large pile right near the lift. Walking slowly he could see the surviving members of Hammer attempting to retreat. _I have to get to them; we can't give up on the crucible. On three I make a sprint for it. One…Two…Three!_

Shepard began sprinting towards the survivors. The pain in his leg was excruciating, any second they felt like they would give in. He wanted to, just to fall down and die. Yet he couldn't, he had come so far, he was so close, he had to end it. The Reapers could not, will not win. _Come on come on come on come on come on come on. Come on Johnny you can do it, you can do it._

Nearing the survivors he saw a laser whizzing over his head, hitting what looked to be an evac shuttle, causing it to careen into a nearby building. Shepard kept on moving finally catching up to one of the remaining soldiers. The soldier looked at Shepard in shock .

"Commander Shepard? You're still alive?" The soldier said incredulously.

"What?"

"Sir, we all saw you get hit by that laser about twenty minutes ago!"

_Okay, so I've been out for twenty minutes, that's not too bad._

"Where is Admiral Anderson?" "He's up in the Citadel sir. When that Reaper was firing at you, the admiral saw a window of opportunity. He saw that the reaper was distracted and managed to get a small squad of six or seven into the lift."

"He got in. That's great! We have to get up there next!"

"How sir? We're pinned down."

"Do you have a radio?" Shepard asked, an idea starting to form in his head.

"Uh yes sir, right here." The soldier handed Shepard his radio. Shepard started tuning the frequency.

"Hello, hello SSV-Normandy, this is Commander Shepard, do you read me, I repeat this is Shepard do you read me?" There was silence for a moment before Jokers voice broke through.

"Commander is that really you?"

"Yes Joker it's me."

"We'd heard that you had been hit and we all feared the worst."

"I'm fine but we need evac now!"

"Okay I'll be there in five."

Shepard turned to the soldier "Alright, we have a ride coming we just need to hold out. How many men do we have?"

The young soldier looked around for a few seconds. "About five of us sir."

"Okay, I need a gun."

"Take my assault rifle sir, I'm better with a sniper rifle anyway."

Shepard took the assault rifle and a few thermal clips the soldier could provide, cocking the weapon into firing mode.

"By the way, what's your name soldier?"

"Corporal Tyler Jenkins, sir."

As Shepard and Jenkins were talking husks began to close in on the group. Shepard and Jenkins popped out of cover, sinking rounds into the faces of the approaching husks. The other soldiers spotted out a group of Marauders setting up flanking points around them. Shepard scanned the filed around them. Noticing strategic weak points he quickly started improvising a plan.

"Does anyone have a grenade?" Shepard called out to the men.

"I do!" "Me too!" "I have three!"

"Fantastic, bring them all here!"

The men handed Shepard all of the grenades that they had on them.

"Ok, now I need a working helmet, someone give me a working helmet!"

"I'll give you mine sir!" One of the soldiers walked up to Shepard, handing him his helmet.

Jenkins walked up to Shepard curiously. "Sir what are you doing?"

Shepard began to break open the helmet, pulling out then reattaching wires, as he explained his plan to Jenkins. "All of these helmets have a radio inside of them. These radios operate on wavelengths. If I could manipulate the wavelengths, I could convert this helmet into a makeshift detonator."

Jenkins began to piece together Shepard's plan at that moment.

"And then you'll manipulate the electric counter in the grenades to delay until given the wavelength, making them into remote control mines!"

"You go it! Now who has an omni-tool?"

Jenkins handed Shepard his omni-tool. "Take mine sir, it's a Polaris VII so it should have enough range."

"Great!"

Shepard attached the omni-tool, activating it and waving it over the grenades. Hacking into their systems he reversed the neutron flow, allowing the grenades to accept the helmet detonation signal. Shepard then took each grenade and carefully tossed them around the little bunker they were all huddled in, effectively creating an explosive perimeter.

"Alright men, take positions around the bunker, try to cover as many sides as possible. We have to hold them off until the Normandy gets her."

All in unison the soldiers replied "Yes Sir!"

The marauders began to attack in unison, covering all possible flanking angles. The soldiers were selective with their shooting waiting until they were able to draw them in, focusing on the gaps in their chest armor. Jenkins began to get worried.

"Commander they're closing in fast, shouldn't you detonate?"

"Not yet, they need to be closer."

The marauders continued to close in, their shields giving them enough protection form the soldiers.

"Commander, I really thin…"

Before the soldier who had given Shepard his helmet was able to finish his sentence he was shot in the head. One of the marauders had gotten off a clean shot on him. His body slumped to the ground, his face completely caved in from the velocity of the shot. Another face for Shepard to remember.

_I'm so sorry friend, I really am._

At that moment Shepard decided the Marauders were close enough. He clicked the little radio switch inside the helmet, activating the grenades. They all exploded in unison producing a brief wall of fire that completely enveloped the Marauders. Shepard and the soldiers and took cover under the rubble that they had been using. Shepard could feel the heat above his head. After a few nervous seconds he looked back up. The marauders had been completely disintegrated, but in the distance he could see an even bigger problem, two brutes were making their way towards the bunker. Shepard looked around.

_If I could get the men up that hill we could hold out until the Normandy gets here._

"Men we have to get up that hill and into those buildings. We should be able to hold off those brutes until the Normandy gets here."

"Yes Sir!"

"And….move!"

Shepard led the charge up the hill with Jenkins and the rest right behind him. As they were running gunfire started whizzing past from behind. _Great, more marauders._

Dodging the enemy fire Shepard and the men were almost to the building when flaming mortar went sailing over their head, striking the building they were running to. The side of the building exploded knocking the men on their feet. Shepard was the first to get up.

"Come on soldiers we have to keep moving!"

Jenkins stood up almost immediately with the rest of the squad following. Shepard led them past the ruined building towards a small row of little shops and cafes. They were all running in a single line in order to reduce the size of the target.

"Move, move, move!" Shepard yelled out, hopping that they had put enough space between them and the brutes in order to regroup and make a plan. As they moved closer to the building a sinister scream rang out. Suddenly a banshee teleported right behind the soldier closest to the back, grabbing him by the throat. Shepard turned around quickly, firing rounds into the banshees chest.

"Let him go!" Shepard screamed, firing wildly at the banshee. The banshee unleashed its signature screech at them men before teleporting away, soldier still in its grip. Shepard stood stunned, knowing he had failed another person. But he had to continue, he had to get to those buildings.

"Keep moving men, if we can get to the roof, we have a better shot of being seen by the Normandy."

Shepard forced open the door leading to the small café, each man filing in one at a time. They checked each room until eventually finding a stair case.

"Alright, let's go up…"

Shepard was interrupted by a shrill screeching noise. The banshee was back. Shepard's heart started pounding in his chest. _Shit…damn it where is Joker?_

"Okay, everyone up the stairs quickly. Jenkins take point." Shepard then threw Jenkins the assault rifle, Jenkins returned the favor giving him a pistol. Shepard loaded up the pistol with a fresh thermal clip and took position behind Jenkins. The soldiers started making their way up the stairs when another shriek rang out. Shepard stopped moving for a moment, looking around trying to see if the banshee was in sight. _This isn't good; Joker needs to get here soon. It has to have been fiv… _Jenkins interrupted his thoughts.

"That screaming is getting closer."

"I know."

The men arrived at the top of the building, only a door separating them from the roof. Thankfully it was still functional and opened when prompted. They walked out onto the roof, Shepard looking around to see if there was any usable cover. Seeing minimal coverage, he decided that he would have to arrange the men in a suppressing formation in case the banshee confronted them on the roof. Shepard arranged the two with shotguns up front, Jenkins with an assault rifle about eight feet behind him, and Shepard to the far back using a sniper rifle.

"Hold this position" Shepard said, attempting to keep the men focused. He could hear them breathing heavily. They were all nervous and he didn't blame them. Finally the banshee appeared breaking down the door that led inside. It started screaming, slowly walking towards the squad.

"Open fire!"

The squad started firing in unison on the Banshee. Despite the damage it was taking, the banshee continued closer and closer to the front line.

"Move back!" the front line slowly moved back continually firing at the banshee. The banshee started warping forward, gaining ground quickly until it was directly in front of the front line. The banshee grabbed another one of the marines, impaling him on its hands, instantly killing it. Another that Shepard had failed. The banshee looked at Shepard next, hissing at him. _Fine, you want me next? Bring it. _

The banshee started walking towards Shepard, hissing and screeching. As it got closer to Shepard it began to generate a biotic projectile in its hand. It fired it at Shepard, almost hitting him if not for his last second combat role to the side.

As Shepard rolled out of the path of the banshees attack, he felt increasing pain in his legs and chest. _Damn it Joker, I can't do this too much longer. _The banshee warped quickly to Shepard grabbing him by the throat and lifting him up in the air, preparing to impale him to with its hand. As it was about to strike, Jenkins ran up behind it wielding a shot gun blasting the banshee in the back of the head, stunning the monster and giving Shepard enough time to shake free. The banshee then turned towards Shepard again generating another projectile before a loud gunshot rang out, and the banshees head violently rocked to the side.

The Normandy came flying in triumphantly, arriving just in time to save him. Shepard could see Garrus and his sniper standing on the loading ramp. _Great, now I'll never hear the end of this. _

"Well hello Shepard, it looks like you could use some help" Garrus called out to Shepard with what had to be as a close to a shit eating grin as a Turian could manage.

"Yeah, yeah Garrus I know, you saved my ass again, how heroic." Shepard replied.

"Why I'm just doing my job."

The Normandy floated only a few feet from the edge of the building. Shepard started walking towards it, with Jenkins close behind. He looked around for the other marine before finding him slumped on the ground missing part of his chest. _The residual energy from when the banshee warped next to him must have done this. I'm so sorry. _That was it, Jenkins and he were the only survivors from HAMMER.

"Jenkins, come on."

Jenkins nodded as he followed Shepard onto the Normandy. Shepard was back home.

**Hey guys I hope you enjoyed this chapter. I tried to make it more action packed than the last one. Also I wanted to show that Shepard was quick on his feet and could improvise, as he did with the grenades. Anyway the story is gonna really start picking up soon and we should be on the Citadel within a few chapters. I would really appreciate feedback on how the story is going, and reviews are always welcome. Thanks everyone and have a great day. **


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